AMBER: Schedule for QM-MM with Amber9/Amber10

From: Francesco Pietra <>
Date: Wed, 29 Aug 2007 23:30:10 -0700 (PDT)

A guidance about the sequence of procedures for QM-MM with Amber9 in the
perspective of Amber10 would greatly help planning at short or medium term.

If - as published - DFTB performs better than other semiempiricals for
conformational problems, should the sequence:

(1) Minimization of solvent alone at const volume, 0K.
(2) Minimization of the whole system at const volume, 0K.
(3) Bringing the whole system slowly to 300K at const volume.
(5) Equilibrating pressure at atmospheric value and md production.
(6) QM-MM AM1 (or MNDO, or PM3 and variants)

start with solvateCap? Or is any way to carry out (1)-(6) with solvateBox (as I
am doing now) and use the results to perform (7) with solvateCap?

If that change of solvation can not be performed, is any time schedule for
Amber10 to become available? If I understand, (1)-(7) could be performed with
solvateBox with Amber10. If so, it might become profitable to wait to carry out
stage (7) until Amber10 becomes available. All that under the presumption
(unchecked from my side) that solvateBox is more efficient than solvateCap.


francesco pietra

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Received on Sun Sep 02 2007 - 06:07:15 PDT
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